Conversion of tropical peat swamp forest to drainage-based agriculture alters greenhouse gas (GHG) production, but the magnitude of these changes remains highly uncertain. Current emissions factors for oil palm grown on drained peat do not account for temporal variation over the plantation cycle and only consider CO2 emissions. Here, we present direct measurements of GHGs emitted during the conversion from peat swamp forest to oil palm plantation, accounting for CH4 and N2O as well as CO2. Our results demonstrate that emissions factors for converted peat swamp forest is in the range 70–117 t CO2 eq ha−1 yr−1 (95% confidence interval, CI), with CO2 and N2O responsible for ca. 60 and ca. 40% of this value, respectively. These GHG emissions suggest that conversion of Southeast Asian peat swamp forest is contributing between 16.6 and 27.9% (95% CI) of combined total national GHG emissions from Malaysia and Indonesia or 0.44 and 0.74% (95% CI) of annual global emissions.